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Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome

Nature Genetics volume 23, pages 305–308 (1999)Cite this article

Abstract

The genomes of higher plants and animals are highly differentiated, and are composed of a relatively small number of genes and a large fraction of repetitive DNA. The bulk of this repetitive DNA constitutes transposable, and especially retrotransposable, elements1,2,3,4,5,6,7. It has been hypothesized that most of these elements are heavily methylated relative to genes, but the evidence for this is controversial. We show here that repeat sequences in maize are largely excluded from genomic shotgun libraries by the selection of an appropriate host strain because of their sensitivity to bacterial restriction-modification systems. In contrast, unmethylated genic regions are preserved in these genetically filtered libraries if the insert size is less than the average size of genes. The representation of unique maize sequences not found in plant reference genomes is also greatly enriched. This demonstrates that repeats, and not genes, are the primary targets of methylation in maize. The use of restrictive libraries in genome shotgun sequencing in plant genomes should allow significant representation of genes, reducing the number of reactions required.

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Figure 1: The maize genome.
Figure 2: Dot-blot hybridizations of cloned sequences in four libraries.
Figure 3: Graphical comparison of clone representation in filtered maize libraries with random rice genomic clones.

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Acknowledgements

We thank R. Gibbs, R. Wilson and J. McPherson for comments on the manuscript; J. Messing and R. Blumenthal for providing bacterial strains; and M. de la Bastide and K. Habermann for invaluable assistance in the technical management of sequencing operations at the Lita Annenberg Hazen Sequencing Center. This work was supported by grant number 97-35300-4564 from the USDA NRI Plant Genome program to W.R.M. and R.A.M.

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Authors and Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA

    Pablo D. Rabinowicz, Cristina Yordan, Lincoln Stein & Robert A. Martienssen

  2. The Lita Annen Hazenburg Genome Sequencing Center, Cold Spring Harbor, New York, USA

    Kristin Schutz, Neilay Dedhia, Laurence D. Parnell & W. Richard McCombie

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  1. Pablo D. Rabinowicz
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  2. Kristin Schutz
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Correspondence to Robert A. Martienssen.

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Rabinowicz, P., Schutz, K., Dedhia, N. et al. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23, 305–308 (1999). https://doi.org/10.1038/15479

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